Genetical research最新文献

Wild populations are smaller than we think: a commentary on 'Effective population size/adult population size ratios in wildlife: a review' by Richard Frankham. 野生种群比我们想象的要小:理查德·弗兰克汉姆对《野生动物的有效种群规模/成年种群规模比率:综述》的评论。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009701

T. Mackay

where H0 is the heterozygosity of the population before the bottleneck, Ht is the heterozygosity after t generations of maintenance with 2N individuals and F is the inbreeding coefficient (Falconer & Mackay, 1996). Clearly heterozygosity decreases, and inbreeding increases, as N decreases ; and these effects accumulate over time. However, no real population fits the ideal model on which this theory is based, which includes self-fertilization in random amounts. The concept of effective population size enables us to utilize this expression by replacing the N in the equation with Ne, where Ne, the effective population size, is the number of individuals that would give rise to the same variance in gene frequency or rate of inbreeding as an ideal population of that size (Falconer & Mackay, 1996). Major departures from the ideal population model that affect Ne are unequal numbers of males and females, unequal numbers of individuals in different generations, non-random distribution of family size, and overlapping generations. Analytical expressions relating the census size of the population (N) to the effective population size have been derived for each of these cases (Frankham, 1995; Falconer & Mackay, 1996) ; under most scenarios Ne

其中，H0为瓶颈前种群的杂合度，Ht为2N个个体维持t代后的杂合度，F为近交系数(Falconer & Mackay, 1996)。显然，随着N的减少，杂合度降低，近交增加;这些影响会随着时间的推移而累积。然而，没有真实的人口符合这一理论所依据的理想模型，其中包括随机数量的自我受精。有效种群规模的概念使我们能够利用这个表达式，将等式中的N替换为Ne，其中Ne是有效种群规模，是与该规模的理想种群在基因频率或近亲繁殖率方面产生相同方差的个体数量(Falconer & Mackay, 1996)。影响Ne的与理想人口模型的主要偏差是男女数量不等，不同世代的个体数量不等，家庭规模的非随机分布以及世代重叠。对于每一种情况，都推导出了有关人口普查规模(N)与有效人口规模的解析表达式(Frankham, 1995;Falconer & Mackay, 1996);在大多数情况下Ne

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引用次数: 3

The Hill-Robertson effect is a consequence of interplay between linkage, selection and drift: a commentary on 'The effect of linkage on limits to artificial selection' by W. G. Hill and A. Robertson. 希尔-罗伯逊效应是连锁、选择和漂移之间相互作用的结果:w·g·希尔和a·罗伯逊对“连锁对人工选择限制的影响”的评论。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009506

Z. Zeng

引用次数: 0

Hybrid dysgenesis: from darkness into light: a commentary on 'Hybrid dysgenesis in Drosophila melanogaster: rules of inheritance of female sterility' by William R. Engels. 杂交发育不良:从黑暗到光明:对威廉·r·恩格斯的《黑胃果蝇的杂交发育不良:雌性不育的遗传规则》的评论。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009609

D. Finnegan

One of the many striking insights to have come from sequencing complete genomes is the realization that transposable elements make up a large proportion of the DNA of most eukaryotes. These elements are far from minor players on the genomic stage. They have had a major role in genome evolution and are a significant source of genome instability. Transposable elements are driven to high copy number by transposition, but their activity is difficult to study experimentally as most copies are defective, and the few that are transpositionally competent move infrequently. This is good for the host organism, but not for anyone wanting to study them. A small number of transposable elements in Drosophila transpose at high levels in the progeny of particular crosses. This results in genetic instability manifest by reduced fertility of one or both sexes and a high frequency of germ line mutations, a phenomenon known as hybrid dysgenesis (Kidwell, 1977). P–M hybrid dysgenesis, for example, is seen when males of a P-type strain are crossed with females of an M-type strain, but not in the progeny of the reciprocal cross. At the heart of hybrid dysgenesis is a breakdown in the control of transposition. This was not immediately apparent and for several years hybrid dysgenesis was regarded as a strange phenomenon that appeared to run counter to accepted ‘ rules ’ of genetics. Bill Engels was one of the first to address this, and his analysis of the genetic basis for the difference between P and M strains established a paradigm for subsequent research (Engels, 1979). In an elegant series of experiments, Engels was able to show that hybrid dysgenesis could be explained by the interaction of polygenic chromosomal factors that appeared to be inherited in a Mendelian fashion, and a maternally inherited cytoplasmic state that he called ‘cytotype’. He proposed that the cytotype of M strain females is permissive for the activity of the chromosomal factors, P factors, which, in dysgenic flies, would be inherited from P strain males. The cytotype of a P strain would be non-permissive, thus accounting for the non-reciprocal nature of hybrid dysgenesis. He further suggested that P cytotype is determined by P factors themselves, explaining why P strains are genetically stable. Finally, he proposed that P factors might be transposable elements, as was thought to be the case for chromosomal factors responsible for a second form of hybrid dysgenesis, I–R hybrid dysgenesis (Picard, 1976). The suggestion that the chromosomal determinants responsible for P–M hybrid dysgenesis are transposable elements was confirmed by the identification of insertions of repeated sequences in the white gene in white-eye mutations isolated from the progeny of P–M dysgenic flies (Rubin et al., 1982). These insertions appeared to be deletion derivatives of a longer element, probably the P factor itself. This was cloned and shown to have P factor activity by injection into M strain embryos, an experiment

从全基因组测序中获得的许多惊人见解之一是认识到转座因子构成了大多数真核生物DNA的很大一部分。在基因组的舞台上，这些元素远不是次要的角色。它们在基因组进化中起着重要作用，也是基因组不稳定的重要来源。转座因子是由转座驱动的高拷贝数，但由于大多数拷贝是有缺陷的，而少数具有转座能力的拷贝很少移动，因此它们的活性很难通过实验研究。这对宿主生物是有好处的，但对任何想要研究它们的人来说都不是。在果蝇中，少数转座因子在特定杂交的后代中有高水平的转座。这导致遗传不稳定，表现为一种或两性的生育能力降低，种系突变频率高，这种现象被称为杂交发育不良(Kidwell, 1977)。例如，当p型株的雄性与m型株的雌性杂交时，可以看到P-M杂交发育不良，但在反向杂交的后代中则不会出现。杂交发育不良的核心是对转位控制的崩溃。这并没有立即显现出来，几年来，杂交发育不良被认为是一种奇怪的现象，似乎与公认的遗传学“规则”背道而驰。比尔·恩格斯是最早解决这个问题的人之一，他对P和M菌株之间差异的遗传基础的分析为随后的研究建立了一个范例(恩格斯，1979)。在一系列优雅的实验中，恩格斯证明了杂交发育不良可以用多基因染色体因素的相互作用来解释，多基因染色体因素似乎是以孟德尔的方式遗传的，而母系遗传的细胞质状态被他称为“细胞型”。他提出，M株雌性的细胞类型允许染色体因子P因子的活性，在基因异常果蝇中，这些因子将遗传自P株雄性。P菌株的细胞型是非允许的，因此说明了杂交发育不良的非互易性质。他进一步提出P细胞型是由P因子本身决定的，这解释了为什么P菌株在遗传上是稳定的。最后，他提出P因子可能是转座因子，就像人们认为的那样，染色体因子负责第二种形式的杂交发育不良，即I-R杂交发育不良(Picard, 1976)。从P-M基因异常果蝇的后代中分离出的白眼突变中，在白色基因中插入了重复序列，证实了导致P-M杂交基因异常的染色体决定因素是转座因子(Rubin et al.， 1982)。这些插入似乎是一个更长的元素的缺失衍生物，可能是P因子本身。这是克隆的，并通过注射到M株胚胎中显示具有P因子活性，这是一个基于Engel对细胞类型在控制P因子活性中的作用的见解的实验。由这些胚胎产生的果蝇表现出杂交后代的一些特征

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引用次数: 1

Genetic variability and neutral mutations: a commentary on 'Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles' by Motoo Kimura. 遗传变异和中性突变:Motoo Kimura对“由于中性和近中性等等位基因的突变产生而在有限种群中保持遗传变异”的评论。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S001667230800952X

D. Gessler

引用次数: 0

Identity and coalescence in structured populations: a commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin. 结构种群的同一性和合并:对Montgomery Slatkin的“近亲繁殖系数和合并时间”的评论。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009683

N. Barton

引用次数: 3

A model in two acts: a commentary on 'A model detectable alleles in a finite population' by Timoko Ohta and Motoo Kimura. 两种行为的模型:对Timoko Ohta和Motoo Kimura的“有限种群中可检测的等位基因模型”的评论。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009543

J. Hey

In the early 1970s, protein electrophoresis was the primary tool geneticists used to discover and measure allelic variation in natural populations. It was a relatively simple and inexpensive technique and, most importantly, it permitted the detection of multiple alleles regardless of polymorphism levels. This was a critical point because before the age of protein electrophoresis, segregating alleles were usually discovered only in cases where clearly discrete patterns of phenotypic variation were first observed. With protein electrophoresis a geneticist’s ability to identify multiple alleles did not depend on a prior indication of the presence of genetic variation (Hubby & Lewontin, 1966; Lewontin, 1974). The purpose of the short paper that Tomoko Ohta and her mentor Motoo Kimura published in Genetical Research in 1973 was to devise a mutation model that was explicitly appropriate for protein electrophoretic data and that would permit such data to be analysed with regard to questions on the relative roles of natural selection and genetic drift. As data on electrophoretic alleles began to accumulate, it was discovered that individuals were heterozygous, and many species were polymorphic, at a substantial fraction of the proteins that could be surveyed. These numbers on heterozygosity and polymorphism immediately began to feed a long-standing hunger, that had built up from decades of sophisticated modelling, for data on such topics as mutation rates, genetic load, the rate of neutral mutations, and the relative roles of natural selection and genetic drift in shaping levels and patterns of variation. Ohta and Kimura were the primary theoreticians of the neutral theory of molecular evolution and they had a very strong interest (as did most population geneticists of that age) in understanding how well the neutral theory explained the levels of polymorphism discovered by electrophoresis. The models they developed focused on amounts and patterns of genetic variation, and they tended to include explicitly a neutral mutation rate as well as assumptions about the nature of the mutation process. One prediction of the neutral theory was that the number of alleles in a population was expected to co-vary strongly with the effective population size. Earlier in 1964, Kimura and James Crow had developed the infinite alleles model, in which every mutation gives rise to a new allele (Kimura & Crow, 1964), and under this model the number of neutral alleles varies linearly with both effective population size and neutral mutation rate. Ohta and Kimura’s key idea in 1973 was a mutation model that explicitly gave rise to new allelic states in single steps that differed in net protein charge. Because four of the amino acids are normally charged at physiological pH, the surface of a soluble protein will carry a charge that affects its behaviour in gel electrophoresis, and mutations that raise or lower this charge will increase or decrease the rate of electrophoresis. In O

在20世纪70年代早期，蛋白质电泳是遗传学家用来发现和测量自然种群中等位基因变异的主要工具。这是一种相对简单和廉价的技术，最重要的是，它允许检测多个等位基因，而不管多态性水平如何。这是一个关键点，因为在蛋白质电泳时代之前，分离等位基因通常只在首次观察到明显离散的表型变异模式的情况下发现。通过蛋白质电泳，遗传学家识别多个等位基因的能力不依赖于遗传变异存在的先前指示(Hubby & Lewontin, 1966;Lewontin, 1974)。1973年，Tomoko Ohta和她的导师Motoo Kimura在《遗传学研究》上发表了一篇简短的论文，目的是设计一个明确适用于蛋白质电泳数据的突变模型，并允许对这些数据进行分析，以解决自然选择和遗传漂变的相对作用问题。随着电泳等位基因的数据开始积累，人们发现个体是杂合的，许多物种是多态的，在可以调查的蛋白质的很大一部分上。这些关于杂合性和多态性的数据立即开始满足长期以来的需求，这种需求是几十年来建立的复杂模型，对突变率、遗传负荷、中性突变率以及自然选择和遗传漂变在形成变异水平和模式方面的相对作用等主题的数据的需求。Ohta和Kimura是分子进化中性理论的主要理论家，他们(和那个时代的大多数群体遗传学家一样)对理解中性理论如何很好地解释电泳发现的多态性水平有着浓厚的兴趣。他们建立的模型关注的是基因变异的数量和模式，而且它们倾向于明确地包括一个中性的突变率，以及对突变过程本质的假设。中性理论的一个预测是，一个群体中等位基因的数量预计与有效群体规模密切相关。早在1964年，Kimura和James Crow就提出了无限等位基因模型，即每次突变都会产生一个新的等位基因(Kimura & Crow, 1964)，在该模型下，中性等位基因的数量随有效种群规模和中性突变率呈线性变化。1973年，Ohta和Kimura的关键思想是一个突变模型，该模型明确地在单个步骤中产生新的等位基因状态，这些等位基因的净蛋白质电荷不同。由于四种氨基酸通常在生理pH值下带电，因此可溶性蛋白质的表面会携带影响其在凝胶电泳中的行为的电荷，而增加或降低这种电荷的突变会增加或减少电泳速率。Ohta和Kimura的模型后来被称为“逐步突变模型”(Kimura & Ohta, 1978)，有时也被称为“阶梯模型”，在该模型中，蛋白质可能在+1和x1步中突变为不同的等位基因状态。重要的是，与无限位点模型不同，在该模型下，两种蛋白质在种类上是相同的(即具有相同的净电荷)，并且由于具有相同等位基因状态的祖先基因的共同血统而不相同(即通过血统而相同)。Ohta和Kimura是微分方程的虚拟动态二人组，在这篇论文中，和其他许多论文一样，他们采用了扩散方程的方法。他们的主要目标是表达一个群体中等位基因的有效数量。在无限位点模型下，Kimura和Crow证明了ne=1+4Neu (Kimura & Crow, 1964)。但是在逐步模型下，Ohta和Kimura发现ne= ffffffffffffffffffffffffffffffffffi

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引用次数: 1

Estimating the recombination parameter: a commentary on 'Estimating the recombination parameter of a finite population model without selection' by Richard R. Hudson. 重组参数的估计:对Richard R. Hudson“估计无选择的有限种群模型的重组参数”的评注。

Genetical research

Pub Date : 2007-12-01 DOI: 10.1017/S0016672308009622

B. Weir

In 1987, Hudson proposed an estimator for the scaled recombination parameter C=4Nc, where N is the population size and c is the recombination rate between the two most distant of a set of segregating sites. This work came shortly after Kreitman (1983) published the first set of population genetic data at the DNA sequence level. Kreitman had been able to sequence 2.7 kilobases of the Drosophila melanogaster genome in 11 samples. It was felt at that time that population genetics was entering a new era, although Hudson cautioned that sufficiently large data sets for his new estimator ‘may require prohibitively large research efforts ’. Hudson’s estimator is based on the variance of the number of site differences between pairs of haplotypes and an estimate of the scaled mutation rate h=4Nm. The variance of the number of differences had already been shown by Brown et al. (1980) to be a convenient single-statistic summary of all the pairwise linkage disequilibria among a set of loci. The need for such a statistic continues as there is still doubt as to how well two-locus associations capture the full multilocus structure. Hudson provided an elegant derivation of the expected value of his statistic as a function of the unknown value C. His method of moments approach to estimation has the great virtue of simplicity although it would not be expected to behave as well as the maximum-likelihood methods that he (Hudson, 1993) and others (e.g. Kuhner et al., 2000; Wall, 2000; Fearnhead and Donnelly, 2001) developed later. Likelihood methods exploit all the information in a data set rather than just the information in a summary statistic and will do well provided the underlying evolutionary model is appropriate for the data being addressed. Writing 10 years after Hudson, Wakeley kept the same moment approach but provided modifications to Hudson’s method that improved its performance. Since 1983 the human genome has been sequenced, as have the genomes of several other species. There is now a ‘1000 genomes’ project (http://www.1000 genomes.org) under way for humans, and new sequencing techniques will make it possible very soon for population geneticists to obtain large samples of DNA sequence data. In 1987, Hudsonwished formore extensive DNA sequence data but he could not have foreseen the remarkable explosion of intermediate data – single-nucleotide polymorphisms (SNPs). Human geneticists are now generating 1 million SNP profiles for samples of thousands of individuals. By 2002, Hudson had produced a simulation procedure for SNP data (Hudson, 2002), and this has been used in studies such as Li and Stephens (2003) to detect recombination rate ‘hotspots ’. Hudson’s 1987 paper has the hallmarks of a classic paper. It introduced a new and simple method for estimating recombination rates from population samples rather than from pedigree data. More sophisticated methods have since been introduced, including composite-likelihood (Hudson, 2001) and others reviewed by H

1987年，Hudson提出了缩放重组参数C=4Nc的估计量，其中N为种群大小，C为一组分离位点中距离最远的两个位点之间的重组率。这项工作是在Kreitman(1983)发表第一组DNA序列水平的种群遗传数据后不久进行的。克雷特曼已经能够在11个样本中对黑腹果蝇基因组的2.7万个碱基进行测序。当时人们认为，群体遗传学正在进入一个新时代，尽管哈德森警告说，足够大的数据集对于他的新估计器来说“可能需要大量的研究努力”。Hudson的估计值是基于单倍型对之间的位点差异数的方差和缩放突变率h=4Nm的估计值。Brown等人(1980)已经证明，差异数的方差是一组基因座中所有成对连锁不平衡的方便的单统计汇总。对这种统计的需求仍在继续，因为对于双位点关联如何很好地捕获完整的多位点结构仍然存在疑问。Hudson提供了他的统计值期望值作为未知值c的函数的优雅推导。他的矩量方法估计具有简单的优点，尽管它不会像他(Hudson, 1993)和其他人(例如Kuhner等人，2000;墙,2000;Fearnhead and Donnelly, 2001)发展较晚。似然方法利用数据集中的所有信息，而不仅仅是汇总统计数据中的信息，如果底层进化模型适合于所处理的数据，它将会做得很好。在哈德逊10年后，韦克利继续沿用了哈德逊的方法，但对哈德逊的方法进行了修改，以提高其性能。自1983年以来，人类基因组已被测序，其他几个物种的基因组也已测序。现在有一个针对人类的“1000个基因组”项目(http://www.1000 genomes.org)正在进行中，新的测序技术将使群体遗传学家很快有可能获得大量DNA序列数据样本。1987年，哈德逊希望获得更广泛的DNA序列数据，但他无法预见到中间数据——单核苷酸多态性(snp)的惊人爆炸式增长。人类遗传学家现在正在为数千个人的样本生成100万个SNP图谱。到2002年，Hudson已经制作了一个SNP数据的模拟程序(Hudson, 2002)， Li和Stephens(2003)等研究已使用该程序来检测重组率的“热点”。哈德森1987年的论文具有经典论文的特点。它提出了一种新的和简单的方法估计重组率从总体样本，而不是从系谱数据。后来引入了更复杂的方法，包括复合似然法(Hudson, 2001)以及Hellenthal和Stephens(2006)评述的其他方法，但最初的方法在进化研究中仍然有用(例如Meikeljohn等人，2004)。

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